musica 0.12.0__cp311-cp311-win32.whl → 0.12.1__cp311-cp311-win32.whl

musica/main.py

@@ -0,0 +1,89 @@
+import argparse
+import datetime
+import logging
+import shutil
+import os
+from musica import Examples
+from musica import __version__
+import musica.examples
+import importlib.resources as ir
+
+
+def format_examples_help(examples):
+    return '\n'.join(f"{e.short_name}: {e.description}" for e in examples)
+
+
+def parse_arguments():
+    parser = argparse.ArgumentParser(
+        description='musica CLI',
+        formatter_class=argparse.RawTextHelpFormatter
+    )
+    parser.add_argument(
+        '-e', '--example',
+        type=str,
+        choices=[e.short_name for e in Examples],
+        help=f'Name of the example to copy out.\nAvailable examples:\n{format_examples_help(Examples)}'
+    )
+    parser.add_argument(
+        '-o', '--output',
+        type=str,
+        action="append",
+        help=("Path to save the example script to.")
+    )
+    parser.add_argument(
+        '-v', '--verbose',
+        action='count',
+        default=0,
+        help='Increase logging verbosity. Use -v for info, -vv for debug.'
+    )
+    parser.add_argument(
+        '--version',
+        action='version',
+        version=f'musica {__version__}',
+    )
+    return parser.parse_args()
+
+
+def setup_logging(verbosity):
+    log_level = logging.DEBUG if verbosity >= 2 else logging.INFO if verbosity == 1 else logging.CRITICAL
+    datefmt = '%Y-%m-%d %H:%M:%S'
+    format_string = '%(asctime)s - %(levelname)s - %(module)s.%(funcName)s - %(message)s'
+    formatter = logging.Formatter(format_string, datefmt=datefmt)
+    console_handler = logging.StreamHandler()
+    console_handler.setFormatter(formatter)
+    console_handler.setLevel(log_level)
+    logging.basicConfig(level=log_level, handlers=[console_handler])
+
+
+def main():
+    start = datetime.datetime.now()
+
+    args = parse_arguments()
+    setup_logging(args.verbose)
+
+    logger = logging.getLogger(__name__)
+
+    logger.debug(f"{__file__}")
+    logger.info(f"Start time: {start}")
+
+    logger.debug(f"Working directory = {os.getcwd()}")
+
+    example = next(e for e in Examples if e.short_name == args.example)
+    if example is None:
+        raise ValueError(f"Example not found: {args.example}")
+    if not args.output:
+        logger.debug("No output path specified, using current directory.")
+
+    logger.info(f"Copying example: {example} to {args.output}")
+
+    with ir.path(musica.examples, example.path) as example_path:
+        logger.info(f"Copying example from {example_path} to {args.output}")
+        shutil.copy(example_path, args.output[0] if args.output and len(args.output) > 0 else '.')
+
+    end = datetime.datetime.now()
+    logger.info(f"End time: {end}")
+    logger.info(f"Elapsed time: {end - start} seconds")
+
+
+if __name__ == "__main__":
+    main()

musica/mechanism_configuration/__init__.py

@@ -1 +1 @@
-from .mechanism_configuration import *
+from .mechanism_configuration import *

musica/mechanism_configuration/aqueous_equilibrium.py

@@ -1,20 +1,24 @@
-from typing import Optional, Any, Dict, List, Union, Tuple
-from musica import _AqueousEquilibrium, _ReactionComponent
-from .phase import Phase
-from .species import Species
+from .utils import _add_other_properties
 from .reactions import ReactionComponentSerializer
-from .utils import _add_other_properties, _remove_empty_keys
+from .species import Species
+from .phase import Phase
+from typing import Optional, Any, Dict, List, Union, Tuple
+from .. import backend
 
+_backend = backend.get_backend()
+_AqueousEquilibrium = _backend._mechanism_configuration._AqueousEquilibrium
+_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
+ReactionType = _backend._mechanism_configuration._ReactionType
 
-class AqueousEquilibrium(_AqueousEquilibrium):
+
+class AqueousEquilibrium:
     """
     A class representing an aqueous equilibrium reaction rate constant.
 
     Attributes:
         name (str): The name of the aqueous equilibrium reaction rate constant.
-        gas_phase (Phase): The gas phase in which the reaction occurs.
-        aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-        aerosol_phase_water (Species): The water species in the aerosol phase.
+        condensed_phase (Phase): The condensed phase in which the reaction occurs.
+        condensed_phase_water (Species): The water species in the condensed phase.
         reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
         products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the reaction.
         A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1].
@@ -26,9 +30,10 @@ class AqueousEquilibrium(_AqueousEquilibrium):
     def __init__(
         self,
         name: Optional[str] = None,
-        aerosol_phase: Optional[Phase] = None,
-        aerosol_phase_water: Optional[Species] = None,
-        reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+        condensed_phase: Optional[Phase] = None,
+        condensed_phase_water: Optional[Species] = None,
+        reactants: Optional[List[Union[Species,
+                                       Tuple[float, Species]]]] = None,
         products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
         A: Optional[float] = None,
         C: Optional[float] = None,
@@ -40,8 +45,8 @@ class AqueousEquilibrium(_AqueousEquilibrium):
 
         Args:
             name (str): The name of the aqueous equilibrium reaction rate constant.
-            aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-            aerosol_phase_water (Species): The water species in the aerosol phase.
+            condensed_phase (Phase): The condensed phase in which the reaction occurs.
+            condensed_phase_water (Species): The water species in the condensed phase.
             reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
             products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the reaction.
             A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1].
@@ -49,53 +54,221 @@ class AqueousEquilibrium(_AqueousEquilibrium):
             k_reverse (float): Reverse rate constant [(mol m-3)^(n-1)s-1].
             other_properties (Dict[str, Any]): A dictionary of other properties of the aqueous equilibrium reaction rate constant.
         """
-        super().__init__()
-        self.name = name if name is not None else self.name
-        self.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
-        self.aerosol_phase_water = (
-            aerosol_phase_water.name if aerosol_phase_water is not None else self.aerosol_phase_water
-        )
-        self.reactants = (
-            [
-                (
-                    _ReactionComponent(r.name)
-                    if isinstance(r, Species)
-                    else _ReactionComponent(r[1].name, r[0])
-                )
-                for r in reactants
-            ]
-            if reactants is not None
-            else self.reactants
-        )
-        self.products = (
-            [
-                (
-                    _ReactionComponent(p.name)
-                    if isinstance(p, Species)
-                    else _ReactionComponent(p[1].name, p[0])
-                )
-                for p in products
-            ]
-            if products is not None
-            else self.products
-        )
-        self.A = A if A is not None else self.A
-        self.C = C if C is not None else self.C
-        self.k_reverse = k_reverse if k_reverse is not None else self.k_reverse
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
+        # Create the internal C++ instance
+        self._instance = _AqueousEquilibrium()
 
-    @staticmethod
-    def serialize(instance) -> Dict:
-        serialize_dict = {
+        # Set all parameters
+        if name is not None:
+            self.name = name
+        if condensed_phase is not None:
+            self.condensed_phase = condensed_phase
+        if condensed_phase_water is not None:
+            self.condensed_phase_water = condensed_phase_water
+        if reactants is not None:
+            self.reactants = reactants
+        if products is not None:
+            self.products = products
+        if A is not None:
+            self.A = A
+        if C is not None:
+            self.C = C
+        if k_reverse is not None:
+            self.k_reverse = k_reverse
+        if other_properties is not None:
+            self.other_properties = other_properties
+
+    # Property delegation to self._instance
+    @property
+    def name(self) -> str:
+        """Get the name of the aqueous equilibrium reaction rate constant."""
+        return self._instance.name
+
+    @name.setter
+    def name(self, value: str):
+        """Set the name of the aqueous equilibrium reaction rate constant."""
+        self._instance.name = value
+
+    @property
+    def condensed_phase(self) -> str:
+        """Get the condensed phase name."""
+        return self._instance.condensed_phase
+
+    @condensed_phase.setter
+    def condensed_phase(self, value: Union[Phase, str]):
+        """Set the condensed phase."""
+        if isinstance(value, Phase):
+            self._instance.condensed_phase = value.name
+        elif isinstance(value, str):
+            self._instance.condensed_phase = value
+        else:
+            raise ValueError(f"Invalid condensed_phase type: {type(value)}")
+
+    @property
+    def condensed_phase_water(self) -> str:
+        """Get the condensed phase water species name."""
+        return self._instance.condensed_phase_water
+
+    @condensed_phase_water.setter
+    def condensed_phase_water(self, value: Union[Species, str]):
+        """Set the condensed phase water species."""
+        if isinstance(value, Species):
+            self._instance.condensed_phase_water = value.name
+        elif isinstance(value, str):
+            self._instance.condensed_phase_water = value
+        else:
+            raise ValueError(f"Invalid condensed_phase_water type: {type(value)}")
+
+    @property
+    def reactants(self) -> List[Union[Species, Tuple[float, Species]]]:
+        """Get the reactants as Python objects."""
+        # Convert from C++ _ReactionComponent objects to Python Species objects
+        result = []
+        for rc in self._instance.reactants:
+            if hasattr(rc, 'coefficient') and rc.coefficient != 1.0:
+                # Create a tuple with coefficient and species
+                species = Species(name=rc.species_name)
+                result.append((rc.coefficient, species))
+            else:
+                # Just the species
+                species = Species(name=rc.species_name)
+                result.append(species)
+        return result
+
+    @reactants.setter
+    def reactants(self, value: List[Union[Species, Tuple[float, Species]]]):
+        """Set the reactants, converting from Python to C++ objects."""
+        cpp_reactants = []
+        for r in value:
+            if isinstance(r, Species):
+                cpp_reactants.append(_ReactionComponent(r.name))
+            elif isinstance(r, tuple) and len(r) == 2:
+                coefficient, species = r
+                cpp_reactants.append(_ReactionComponent(species.name, coefficient))
+            else:
+                raise ValueError(f"Invalid reactant format: {r}")
+        self._instance.reactants = cpp_reactants
+
+    @property
+    def products(self) -> List[Union[Species, Tuple[float, Species]]]:
+        """Get the products as Python objects."""
+        # Convert from C++ _ReactionComponent objects to Python Species objects
+        result = []
+        for rc in self._instance.products:
+            if hasattr(rc, 'coefficient') and rc.coefficient != 1.0:
+                # Create a tuple with coefficient and species
+                species = Species(name=rc.species_name)
+                result.append((rc.coefficient, species))
+            else:
+                # Just the species
+                species = Species(name=rc.species_name)
+                result.append(species)
+        return result
+
+    @products.setter
+    def products(self, value: List[Union[Species, Tuple[float, Species]]]):
+        """Set the products, converting from Python to C++ objects."""
+        cpp_products = []
+        for p in value:
+            if isinstance(p, Species):
+                cpp_products.append(_ReactionComponent(p.name))
+            elif isinstance(p, tuple) and len(p) == 2:
+                coefficient, species = p
+                cpp_products.append(_ReactionComponent(species.name, coefficient))
+            else:
+                raise ValueError(f"Invalid product format: {p}")
+        self._instance.products = cpp_products
+
+    @property
+    def A(self) -> float:
+        """Get the pre-exponential factor."""
+        return self._instance.A
+
+    @A.setter
+    def A(self, value: float):
+        """Set the pre-exponential factor."""
+        self._instance.A = value
+
+    @property
+    def C(self) -> float:
+        """Get the exponential term."""
+        return self._instance.C
+
+    @C.setter
+    def C(self, value: float):
+        """Set the exponential term."""
+        self._instance.C = value
+
+    @property
+    def k_reverse(self) -> float:
+        """Get the reverse rate constant."""
+        return self._instance.k_reverse
+
+    @k_reverse.setter
+    def k_reverse(self, value: float):
+        """Set the reverse rate constant."""
+        self._instance.k_reverse = value
+
+    @property
+    def other_properties(self) -> Dict[str, Any]:
+        """Get the other properties."""
+        return self._instance.other_properties
+
+    @other_properties.setter
+    def other_properties(self, value: Dict[str, Any]):
+        """Set the other properties."""
+        self._instance.other_properties = value
+
+    @property
+    def type(self):
+        """Get the reaction type."""
+        return ReactionType.AqueousEquilibrium
+
+    def _create_serialize_dict(self, instance) -> Dict:
+        """
+        Helper method to create the serialization dictionary.
+
+        Args:
+            instance: The instance to serialize (either self._instance or a _AqueousEquilibrium object).
+
+        Returns:
+            Dict: Base serialization dictionary.
+        """
+        return {
             "type": "AQUEOUS_EQUILIBRIUM",
             "name": instance.name,
-            "aerosol phase": instance.aerosol_phase,
-            "aerosol-phase water": instance.aerosol_phase_water,
+            "condensed phase": instance.condensed_phase,
+            "condensed-phase water": instance.condensed_phase_water,
             "reactants": ReactionComponentSerializer.serialize_list_reaction_components(instance.reactants),
             "products": ReactionComponentSerializer.serialize_list_reaction_components(instance.products),
             "A": instance.A,
             "C": instance.C,
             "k_reverse": instance.k_reverse,
         }
+
+    def serialize(self) -> Dict:
+        """
+        Serialize the AqueousEquilibrium object to a dictionary using only Python-visible data.
+
+        Returns:
+            Dict: A dictionary representation of the AqueousEquilibrium object.
+        """
+        serialize_dict = self._create_serialize_dict(self._instance)
+        _add_other_properties(serialize_dict, self.other_properties)
+        return serialize_dict
+
+    @staticmethod
+    def serialize_static(instance) -> Dict:
+        """
+        Static serialize method for compatibility with C++ _AqueousEquilibrium objects.
+
+        Args:
+            instance: The _AqueousEquilibrium instance to serialize.
+
+        Returns:
+            Dict: A dictionary representation of the AqueousEquilibrium object.
+        """
+        # Create a temporary AqueousEquilibrium object to use the helper method
+        temp_aqueous_equilibrium = AqueousEquilibrium()
+        serialize_dict = temp_aqueous_equilibrium._create_serialize_dict(instance)
         _add_other_properties(serialize_dict, instance.other_properties)
-        return _remove_empty_keys(serialize_dict)
+        return serialize_dict